1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
|
# SETUP
[ 'rubygems', 'redis', 'opentox-ruby-api-wrapper' ].each do |lib|
require lib
end
case ENV['RACK_ENV']
when 'production'
@@redis = Redis.new :db => 0
when 'development'
@@redis = Redis.new :db => 1
when 'test'
@@redis = Redis.new :db => 2
@@redis.flush_db
end
set :default_content, :yaml
helpers do
def create_dataset(uri)
@@redis.set_add "datasets", uri
end
def add_feature(dataset_uri, compound_uri, feature_uri)
@@redis.set_add dataset_uri + '::compounds', compound_uri
@@redis.set_add dataset_uri + '::features', feature_uri
@@redis.set_add dataset_uri + '::' + compound_uri + '::features', feature_uri
@@redis.set_add dataset_uri + '::' + feature_uri + '::compounds', compound_uri
end
def delete_dataset(uri)
@@redis.set_members(uri + '::compounds').each do |compound_uri|
@@redis.delete uri + '::' + compound_uri
end
@@redis.delete uri + '::compounds'
@@redis.set_members(uri + '::features').each do |feature_uri|
@@redis.delete uri + '::' + feature_uri
end
@@redis.delete uri + '::features'
@@redis.set_delete "datasets", uri
end
def not_found?
halt 404, "Dataset \"#{params[:name]}\" not found." unless @@redis.set_member? "datasets", uri(params[:name])
end
def uri(name)
uri = url_for("/", :full) + name.gsub(/\s|\n/,'_')
end
end
## REST API
get '/?' do
@@redis.set_members("datasets").collect{|d| uri(d)}.join("\n")
end
get '/:name' do
not_found?
@dataset = {:uri => uri(params[:name]), :name => params[:name]}
respond_to do |format|
format.yaml { @dataset.to_yaml }
format.xml { builder :dataset }
end
end
get '/:name/name' do
not_found?
URI.decode(params[:name])
end
get '/:name/compounds' do
not_found?
@@redis.set_members(uri(params[:name]) + "::compounds").join("\n")
end
get '/:name/features' do
not_found?
@@redis.set_members(uri(params[:name]) + "::features").join("\n")
end
=begin
get '/:name/:type/*/*/intersection' do
# CHECK/TEST
@@redis.set_intersect(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
end
get '/:name/:type/*/*/union' do
# CHECK/TEST
@@redis.set_union(params[:splat][0], params[:splat][1], URI.encode(params[:name]) + '/' + params[:type]).join("\n")
end
=end
get '/:name/*/features' do
not_found?
# re-escape smiles (Sinatra unescapes params and splats)
compound_uri = params[:splat].first.sub(%r{(http://[\w\.:]+/)(.*)$}) {|s| $1 + URI.escape($2, /[^#{URI::PATTERN::UNRESERVED}]/)}
#puts compound_uri
@@redis.set_members(uri(params[:name]) + '::' + compound_uri + '::features').join("\n")
end
get '/:name/*/compounds' do
not_found?
@@redis.set_members(uri(params[:name]) + '::' + params[:splat].first + '::compounds').join("\n")
end
post '/?' do
#protected!
uri = uri(params[:name])
halt 403, "Dataset \"#{name}\" exists - please choose another name." if @@redis.set_member?("datasets", uri)
@@redis.set_add "datasets", uri
if params[:file]
File.open(params[:file][:tempfile].path).each_line do |line|
record = line.chomp.split(/,\s*/)
compound_uri = OpenTox::Compound.new(:smiles => record[0]).uri
feature_uri = OpenTox::Feature.new(:name => params[:name], :values => {:classification => record[1]}).uri
add_feature(uri, compound_uri, feature_uri)
end
end
uri
end
put '/:name/?' do
#protected!
not_found?
uri = uri(params[:name])
add_feature(uri, params[:compound_uri],params[:feature_uri])
uri + " sucessfully updated."
end
delete '/:name/?' do
# dangerous, because other datasets might refer to it
#protected!
not_found?
uri = uri(params[:name])
delete_dataset(uri)
"Successfully deleted dataset \"#{uri}\"."
end
|
